Computational Chemistry

Research Update: September 2018

Sep 9, 2018

The arrival of a new batch of freshmen is a sure sign of autumn and the start of a new academic semester. I am thrilled to announce that this semester should also be my last one as a Ph.D. candidate because I officially submitted my dissertation for preliminary examination last week. In this post, I will look back on summer 2018 and recap the research projects that I completed during that time.

Integrating Google Colaboratory into Your Machine Learning Workflow

Sep 9, 2018

Are you using Jupyter notebooks regularly in your machine learning or data science projects? Did you know that you can work on notebooks inside a free cloud-based environment with a GPU accelerator? In this post, I will introduce you to Google Colaboratory and show you in a few simple steps how to integrate this platform into your daily workflow.

Visualizing Geographic Statistical Data with Google Maps

Aug 8, 2018

This tutorial will teach you how to create a custom Google Maps based map for visualizing geographic statistical data. Such maps can be a useful tool when developing machine learning models. As a specific example case, we will create a map for visualizing the population density and median household income of postal code areas in Finland.

Matrix diagonalization in parallel computing: Benchmarking ELPA against ScaLAPACK

May 5, 2018

Matrix diagonalization is a fundamental linear algebra operation with a wide range of applications in scientific and other fields of computing. At the same time, it is also one of the most expensive operations with a formal computational complexity of $\mathcal{O}(N^3)$, which can become a significant performance bottleneck as the size of the system grows. In this post, I will introduce the canonical algorithm for diagonalizing matrices in parallel computing to set the scene for today’s main topic: improving diagonalization performance. With the help of benchmark calculations, I will then demonstrate how a clever mathematical library choice can easily reduce the time needed to diagonalize a matrix by at least 50 %.

A recap of the CP2K-UK 2018 meeting

Jan 1, 2018

The 2018 edition of the CP2K UK user meeting was held two Fridays ago at the University of Lincoln, UK. I will be recaping my experiences of the event in this post.

Constrained DFT tutorial at the CP2K-UK 2018 meeting

Dec 12, 2017

I will be giving an introductory how-to talk on constrained DFT at the 2018 CP2K UK User meeting at the University of Lincoln, UK, on Friday January 12 2018.

Parallelizing I/O operations with MPI, Part 2: Performance tuning and Cray Burst Buffer

Dec 12, 2017

In my previous post, I discussed the benefits of using the message passing interface (MPI) to parse large data files in parallel over multiple processors. In today’s post, I will demonstrate how MPI I/O operations can be further accelerated by introducing the concept of hints. The second topic I will discuss is the emergence of solid-state drives in high-performance computing systems to resolve I/O bottlenecks. These topics will be illustrated by benchmark calculations using a parallel writer routine that I will implement to the task described previously.

Parallelizing I/O operations with MPI: A case study with volumetric data

May 5, 2017

Lately, parsing volumetric data from large (> 300 MB) text files has been a computational bottleneck in my simulations. Because I expect to be processing hundreds of these files, I decided to parallelize the parser routine by leveraging the message passing interface (MPI). I will describe my first experience with MPI I/O in this post by going through the synthesis process of the parallelized parser routine. I will also examine the performance of the parallel parser.

Building CP2K on a Cray XC40

Apr 4, 2017

Compiling a CP2K binary – the massively parallel, open-source quantum chemistry and solid state physics program written in Fortran 2003 – can be a daunting task if you’ve never built a large project using maketools. This post aims to demystify the build process by showcasing a full CP2K build on a Cray XC40 supercomputer (codename Sisu) including dependencies.

Welcome to my website!

Feb 2, 2017

Greetings and welcome! You have stumbled upon the personal website and blog of Nico Holmberg, a 26 year old Finn pursuing a doctoral degree in Computational Quantum Chemistry. Feel free to check out my profile for more information about me, my professional projects and other interests!